


Exodus of the Daleks

by DalekPrime



Series: The Dalek Prime Series! [1]
Category: Brooklyn Nine-Nine (TV), Doctor Who, Doctor Who (1963), Doctor Who (2005), Doctor Who (Big Finish Audio), Faction Paradox (Books & Audio)
Genre: Alternate Universe - Brooklyn Nine-Nine (TV) Fusion, Alternate Universe - Doctor Who Fusion, Crossover, Daleks are erased from the timeline, Episode: The Day of the Doctor, Episode: s04e16 The Waters of Mars, Episode: s04e17-e18 The End of Time, Faction Paradox (Doctor Who), Fourth Doctor Era, Inspired by Brooklyn Nine-Nine (TV), Other, Outer Space, Pre-Time War (Doctor Who), Referenced Time War (Doctor Who), Serial: s050 The War Games, Serial: s078 Genesis of the Daleks, Skaro, Temporal Paradox, The Doctor & The Master (Doctor Who) Friendship, The Void, Time War (Doctor Who), War In Heaven (Faction Paradox)
Language: English
Status: In-Progress
Published: 2020-12-20
Updated: 2021-01-20
Packaged: 2021-03-10 19:40:07
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 2,366
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/28192578
Author URL: https://archiveofourown.org/users/DalekPrime/pseuds/DalekPrime
Summary: “Out of any good must come something evil!”There are ten thousand humans in stasis aboard Starship Nine-Nine. Ten thousand humans expecting to wake up on a new colony. But halfway along the journey, something goes wrong, something terrible, and the entire ship is held hostage.Who is John Kelly, really?How did Dalek Prime get on the ship?What is the Exodus of the Daleks?The Doctor and the Squad must answer these questions and save Starship Nine-Nine.
Relationships: Jake Peralta/Amy Santiago
Series: The Dalek Prime Series! [1]
Series URL: https://archiveofourown.org/series/2065350
Comments: 2
Kudos: 1
Collections: The Supreme Minds Of Skaro





	1. Starship Nine-Nine

**Author's Note:**

  * Inspired by [Genetics of the Daleks](https://archiveofourown.org/external_works/728841) by Jonathan Morris. 



The cryostasis chamber defrosted as the executive officer stepped back from the controls.

“Ugh. That was extremely uncomfortable.” The man said as he awoke from his sleep.

“Hello, can you tell me your name?”

“Officer Jake Peralta.”

“I’m your executive officer, Terrence Jeffords. Welcome aboard Starship Nine-Nine.” He was a large, muscular black man, Jake was a bit threatened by him, but at the same time, a bit comforted by his presence.

He tried getting out of the chamber but found that he was stuck, “I can’t get out.”

“I’ll help you out in a moment, there’s something I have to handle first.” He walked over to the pod near his and began typing into the keypad.

“What are you doing?”

“Awakening your partner.”  
“My partner?” Jake asked, shocked, “With all due respect Terry, I can handle myself; I don’t need a partner.”

“It doesn’t matter what you think; you’re getting a partner.”

The capsule opened revealing a Latina woman with raven black hair, Jake thought she looked quite cute shivering from the cold.

“Brrrrrrrr. S-s-sooo c-c-c-c-cold-d-d.”  
“I’m Executive Officer Terrence Jeffords. Can you tell me your name?”

She waits a minute to warm up before answering him, “Officer Amy Santiago, sir.”

He helps her then Jake out of the pod and guides them to the storage facility to get their stuff. Jake sneaked a peek at Amy’s stuff and stifled a laugh how it was all meticulously organized.

“What?”

“It’s just your stuff is so organized.”  
“It makes finding things more efficient. Much better than your pile stuff.”  
“Hey! I’ll have you know that I have a system.”  
“What? Throw everything randomly into a pile.”

“Well, yeah.”

They didn’t talk much after that and each took their stuff and went to their separate cabins.

Jake napped for a bit and then left to the bridge for the squad briefing. He arrived to everyone already there.

“You’re late.” A black stoic figure in a captain’s uniform spoke.

“You’re not McGinley.”

“Astute observations officer. Captain McGinley had sustained an injury and was forced to undergo cryosleep early.”

“Oh. I thought there was a robot revolution on the ship and he was replaced by a robot, which I still believe is partially true.” He then notices the redhead next to the captain.

“Gina! You haven’t aged a day.” The woman replied, “You know I’m a Goddess gurl.” To this Jake laughed.

“Please hold reunions till the end.”  
“Robot.” Jake half-whispered.

“That is enough. Next time I see you I expect you to be in full uniform.”

“Actually, our original captain didn’t care if we were in uniform.”

“Well, your new captain does. And more importantly, he cares that you follow his direct orders. Everyone, I’m your new commanding officer, Captain Ray Holt.”

“Speech!” Amy shouted out.

“That was my speech.”  
“Short and sweet.”

“Now, now Raymond, don’t be so cold.” A tall old white man with a sinister-looking candy cane smile walked in saying.

“I’m Science Commander John Kelly, Captain Raymond Holt’s boss.” He then left but Jake had a suspicious feeling about him and decided that he’ll be keeping an eye on him.

***

Down in the lab Commander Kelly was working on his current project.

“Do they suspect anything?” The Dalek’s grainy robotic voice spoke up. It was an older model with a black casing, yet it had been in many battles, with scratches and rust across its casing, and its gunstick bent.

“Of course not,” Kelly responded chuckling.

“Good. Soon it will be time to move onto phase two.”  
“Are you sure? The device isn’t ready yet.” He spoke gesturing to a large metallic hexagonal pyramid where instead of the tip there was a tall antenna with a sphere halfway up, the sides of the pyramid being covered in metallic semispheres.

“Do not doubt Dalek science! Dalek science is superior!”

Kelly responded fearfully “no, no, no, I wasn’t doubting you, I was just curious; I have quite an interest in the sciences.”

“Once the gateway is finished, the Dalek Empire will be restored.”  
“And I’ll be in command of the colony ship?”  
“Affirmative.”

***

It’s been three months and Jake already feels at home on Starship nine-nine; in fact, it’s the first place that’s ever felt like home to him. Terry, while large and threatening is truly kind and caring. Rosa Diaz, he was friends with back at the academy, and while she is quiet and scary he knows she’ll always have his back. Charles Boyle while being overly enthusiastic makes up for it by being Jake’s biggest fan. Gina, while narcissistic to a fault is like a sister to him. Hitchcock and Scully are disgusting yet the place wouldn’t be the same without them. Even Holt, who Jake originally thought of as a bother, has become a father figure to him, _something he will never admit._

Amy Santiago though was hard to describe. _Where to begin?_ She’s controlling, and a teacher’s pet, yet competitive and yearns to do what’s right. Jake doesn’t really know what to make of her, case in point their fight right now.

It all began with them discussing in the breakroom why they joined the mission.

“I originally wanted to be a police detective,” spoke Jake, “But there’s not as big a need for them back on Earth so this is the next best thing.”  
“Oh cool. Most of my family is actually in law enforcement. Why did you want to be a cop?”

“ I wanted to be a cop because my favorite movie was Die Hard.”

To this, Amy snorted, “Die Hard? That came out over four hundred years ago. Wow, you are a grandpa.”  
“Says the person who fills out paperwork by hand, holo displays have been invented!”

They continued this childish bickering until Holt came in.

“Captain!” Amy called out, standing in attention.

“There’s been some energy fluctuations in section D3. It’s probably nothing, but I need two officers to check it out.”

Terry responded from the corner eating his yogurt, “Santiago, Peralta, you two finished eating, go check it out.”

Jake quickly got up, turned to Amy and said, “Bet I can get there before you.” and sped off.


	2. The Doctor is in

_ Vrwoop! Vrwoop!  _ The TARDIS slowly materialized onto the ship and the Doctor stepped out, yelling, “You can’t just redirect my TARDIS so that I can solve some problem for you! I’m not your errand boy!” He flipped his scarf around his neck and mumbled under his breath, “Time Lords. You’re lucky I’m so curious, else I wouldn’t stay.”

He walked around checking out the cryostasis chambers until he stopped in front of one and began inspecting it.

“Now that’s interesting, this chamber’s been opened.”

“Of course it has, as you just got out of it, stowaway.” A man spoke holding a gun to him.

“Not your best work.” The woman to his side commented.

“Yeah, I regretted it as soon as I said it.”

“Captain, you’re not going to believe this but…”

“What is it, Officer Santiago,” a man spoke over the comms.

“We’ve found a stowaway.”

***

“Who are you?” Captain Holt asked in his usual inexpressive voice.

“I’m the Doctor, and I’ve come to help.”

“Help?” Rosa asked as if she was partially insulted.

“Yes, help. With anything at all. So please don’t be shy.”

“While we appreciate the offer, Doctor, we have no need for a medical professional.”

“Not only medicinal problems,” he said while taking out a bag of some snack he begins to eat, “Like I said, anything at all.” He paused for a moment and then opened the bag towards them and asked, “Would you like a jelly baby?”

“Well don’t mind if I do,” Jake said as he went to take some jelly babies out of the bag. Amy though quickly slapped his hand away. He cradled his speaking in a surprised manner, “Wow, you’re strong. What did you do that for? It’s not like I was breaking a rule.”

“They could have been poisoned.” Amy responded exasperatedly.

“No they can’t.”

“Yes they can.”

“No they can’t as he ate them, and if they were poison he wouldn’t eat them.” Jake stated matter of factly.

“Guys, enough!” Terry yelled over them.

“Yes, Jeffords is right, please stop your bickering.” Holt spoke, “ Now you called yourself the Doctor, but what’s your name?”   
“The Doctor, just the Doctor.”

“The Doctor?”

“Yes.”

“Just the Doctor?”

“Yes.”

“I’m confused.” Piped in Jake, “Doctor Who?” The Doctor shakes his head a bit until Holt interrupted, “How did you get on Starship Nine-Nine,  _ Doctor _ ?” Jake could tell that calling him  _ the Doctor  _ bothered the Captain.

“Well I’m afraid you wouldn’t believe me if I told you.”   
“Peralta, Santiago, please take the Doctor to a cell.”

“Yes sir.” Responded Santiago a bit too enthusiastically.

“Doctor, please cooperate and hand all items you have on your person to Officer Boyle.”

“Why of course. Could you just answer me this one question?” Asked the doctor, “What year is it?”   
“Two thousand four hundred and thirty-three.”

“No.” The Doctor is shocked, “That can’t be right; this ship is too advanced for the current time period.”   
“Well Science Commissioner Kelly has made modifications to this ship making it the most advanced of its kind.” Holt responded, rolling his eyes at the mention of John Kelly.

“Interesting.” Responded the Doctor, “Can I meet him?”

“You will not as you are a prisoner. Officer Boyle!” A below average sized man with a bit of a chubby face stepped forward, “Please take any items on his person and escort him to a cell.”   
“Take any items on his person and escort him to a cell, title of your sextape.” Jake quipped as the Doctor handed over his sonic and was carried away.

***

Down below in the laboratory the surveillance screen showing what was happening up above switched off.

“The Doctor is here.” Spoke the Dalek.

“Yes. His fourth incarnation if I might add.”

“We must exterminate him!”

“Now, now, let’s not be so hasty.” Kelly responded chuckling.

“He is a threat to the Exodus.”

“Yes. But if we kill him, the rest of the crew will realize something is up and bring an end to machinations. We need to be smart.”

“What do you advise?”

“We need to shut down the cell he’s in and lead him to us. If someone else attempts to kill him he’ll simply regenerate so I need to kill him using this.” He took out a hand held device, “My tissue compression eliminator.”

And so the Dalek and John Kelly set in motion the trap for the Doctor as the crewmembers above were unaware of what was coming, simply doing their everyday tasks as the Exodus approached.


	3. Breakout

**Notes for the Chapter:**

> Please leave comments and Kudos.  
> Thank You

The Doctor sat against the wall of his small metallic cell, the lasers humming lowly, telling himself a story, “...and so Smith turned to the Silurian and said…” Suddenly the lasers keeping him locked in shut off.

“Huh,” The Doctor spoke, getting up to stick his hand through the opening, “It appears I am no longer locked in.” He paused for a moment, thinking, “Either I have a friend somewhere on this ship that’s looking out for me, or I have an enemy; knowing my look and based on the current situation it’s probably an enemy.”

He walks out of his cell patting himself down.

“If I’m going to have to face an adversary I’ll need my sonic and scarf, I suppose I’ll have to request it back.”

He walks down the passage looking for a com to contact the crew when something catches his attention; He sniffs the air around him.

“Something is wrong; I thought I noticed something when I first arrived, especially considering the advanced technology, but now I’m sure of it, there’s a paradox.”

He walked slowly, as if expecting someone to jump up and try to attack him; he was apprehensive. The lights in the hall began to flicker, one specifically caught his attention, it blinked on a series of four; in response to this the Doctor became scared, he could feel his hearts beating.  _ Thump thump thump thump. Thump thump thump thump. _

_ The voices. _ He could hear them. Side effects of him being near the paradox.

_ I don’t care who you are! The Time Lord Victorious is wrong! _

_ No more. _

_ I could do so much more. _

_ Too late. She pressed the wrong button Doctor. _

_ Well, the final responsibility is mine. And mine alone. _

_ The noise, the drumbeat, louder than before. _

_ You’re wasting time, Doctor. _

His head began spinning.

“No. No! Stop it. I tell you, stop it now!” And as if it listened to the Doctor’s request, it did. So the Doctor kept walking on, looking for a way to contact the crew.

***

Below in the laboratory, Dalek Prime reminisced as John Kelly was working on the gate. It used to be  _ Emperor of the Daleks _ . Yet now there is no Dalek Empire, there never was; all that is left of the empire is one Dalek that shouldn’t exist.

“Damnit!” cried out John Kelly, pulling the Dalek out of its reminiscence, as there was a large spark and smoke starting to come out from the equipment.

“What is it?” Asked the Dalek.

“The anti-time generator overloaded, without it we can’t form a link to the past. I’ll need to steal some materials from storage but I should be able to configure it again.”

The Dalek thought for a moment and then spoke up in its grainy voice, “You must make sure not to overload it again.”

“Yes.” John Kelly replied. “Unfortunately eleven-dimensional super-wave equations were never my strong suit.”

He suddenly had an idea and turned to Dalek Prime, “Say, can you solve the energy requirement for the equation  _ 𝛴(ϕ))(((<: _ ?”   
The Dalek thought for a moment and then replied, “Affirmative, the energy requirement is A5763.8B76iJ.”

A light on the wall started flashing, Kelly quickly rushed to his computer to check it out.

“What is it?”

He began to laugh, “The Doctor has left his cell, finally. I’m going to go deal with him, you stay here and recalibrate the equipment.”

So he left a Dalek to its own devices while he went out to hunt the Doctor.

**Author's Note:**

> The original idea for a B99 Doctor Who crossover came after listening to Doctor Big Finish Audio Adventures Mutually Assured Destruction when the author described the prompt as 'Die Hard on a Dalek Timeship'.


End file.
